/ 
onto-perl-0.30
/ CCO::Parser::GoaParser

parse

Usage    - $GoaParser->parse()
Returns  - An CCO::Util::GoaAssociationSet object
Args     - GOA associations file
Function - converts a GOA associations file into a CCO::Util::GoaAssociationSet object

work

Usage    - $GoaParser->work($ref_file_names, 'Arabidopsis thaliana organism')
Returns  - updated CCO::Core::Ontology object 
Args     - 1. reference to a list of filenames(input OBO file, output OBO file, GOA associations file, CCO_id/Uniprot_id map file one taxon only, CCO_id/Uniprot_id map file all taxa), 2. taxon_name
Function - parses a GOA associations file, adds relevant information to the input  ontology, writes OBO and map files

NAME

CCO::Parser::GoaParser - A GOA associations to OBO translator.

DESCRIPTION

Includes methods for adding information from GOA association files to ontologies GOA associations files can be obtained from http://www.ebi.ac.uk/GOA/proteomes.html

The method 'parse' parses the GOA association file and returns a CCO::Util::GoaAssociationSet object

The method 'work' incorporates OBJ_SRC, OBJ_ID, OBJ_SYMB, SYNONYM, DESCRIPTION into the input ontology, writes the ontology into an OBO file, writes map files.

Assumptions: 1. the ontology contains already the term 'protein' 2. the ontology already contains all and only the necessary GO terms. 3. the ontology already contains the NCBI taxonomy. 4. the ontology already contains the relationship types 'is_a', 'participates_in', "derives_from" 5. the input GOA association file contains entries for one species only and for GO terms present in the input ontology only

AUTHOR

Vladimir Mironov vlmir@psb.ugent.be

COPYRIGHT AND LICENSE

Copyright (C) 2006 by Vladimir Mironov

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.